IBD Sharing between Africans, Neandertals, and Denisovans

This site contains supporting material to the
manuscript "IBD Sharing between Africans, Neandertals, and Denisovans".

Summary

Interbreeding between ancestors of humans and other hominins outside of Africa has been
studied intensively, while their common history within Africa still lacks proper
attention.
However, shedding light on human evolution in this time period about which little is
known, is essential for understanding subsequent events outside of Africa.

We investigate the genetic relationships of humans, Neandertals, and
Denisovans by identifying very short DNA segments in the 1000 Genomes Phase 3 data that
these hominins share identical by descent (IBD).
By focusing on low frequency and rare variants, we identify very short IBD segments with
high confidence. These segments reveal events from a very distant past because
shorter IBD segments are presumably older than longer ones.
We extracted two types of very old IBD segments that are not only shared among humans,
but also with Neandertals and/or Denisovans.
The first type contains longer segments that are found primarily in Asians and
Europeans where more segments are found in South Asians than in East Asians for both
Neandertal and Denisovan. These longer segments indicate complex admixture events
outside of Africa.
The second type consists of shorter segments that are shared mainly by
Africans and therefore may indicate events involving ancestors of humans and other
ancient hominins within Africa.
Our results from the autosomes are further supported by an analysis of chromosome X,
on which segments that are shared by Africans and match the Neandertal
and/or Denisovan genome were even more prominent.

Our results indicate that interbreeding with other hominins was a common
feature of human evolution starting already long before ancestors of
modern humans left Africa.

Data and Scripts

Analysis box for doing your own analysis of IBD segment
sharing between humans, Denisovan, and Neandertal:
All the data has been prepared for the analysis of short IBD sharing between
humans, Denisovans, and Neandertals. R-scripts, which are used to
generate the results and the plots of the manuscript and the supplementary information, are provided here.